I was playing around with Caliber this morning, so I thought I'd make a few suggestions, these are just things that I notice and may be of no interest at all to others, still if they can make a great program better.....

Changing Settings - Have a Restart Button.
Reason: If you have just changed settings and a restart is required, it would be nice to have a restart button right there.

Plugin window - Make an entry for "User installed Plugins" -
Reason: so you don't have to search through the whole list to try find one you installed and forgot the name of. None of the other many many plugins that are there are of no real intrest to the average user, they just want to find the one they installed and see its settings, and add or remove it.

Book details window "popout view" - its set at # of pixels wide for the left text portion of the window, allow this to be changed via dragging.
Reason: When double clicking on the book details window, user is after a better view of that info, but all that can be changed is the size of the left image and not the area where all the info is.

Edit Metadata window - Grey/White scheme needs a tweek (Changing picture and comments background to grey would work)
Reason: 1 - Looking to the left of "change cover" and "Comments" there are grey anomilitys that dont look very asthetic, neither does the vertical lines they emminate from.
Reason: 2 - When user is changing the image there, its displayed on a white background, this results in it being impossible to see if the image has any little white borders around it. Which if your as OCC as me will erk you no end when you go into the black background of cover view.
Reason: 3 - The Comments field is White - The Book details are shown on Grey, obviously this will cause visual issues - as it may look fine when editing and filling in the data, but when finished and viewing in "book details" view it looks totally different.

Additional Suggestion

Series - Have set Series entries for certain book types (or certain entrys have no number prefix)
Reason: When sorting through books you most likely have one of these;
A Novel
A Collection
An Omnibus
A Book in a Series
A Short Story (Novella, Chapterbook, Short Story, etc)

Series Books work fine, but what if you want to label your novels, as "Novels, so as not to get them mixed up with you short stories, and for easy reference?

It would be a real neat solution if the Series column could have some set titles, that have no Number associated. If this is possible in the scope of the program.
Just entering Novel or Collection yourself results in the books being incremented, and selecting a group of them results in them all having a [1]
Other way is to have another custom column. too many of those will melt your brain

Oh While I'm here.

Edit Metadata Picture Adding - Stop Selection Jumping
Reason: When in Edit metadata window, Downloading Covers, you have set a limit on the time you want the search to take, which is fine say 15seconds. You have set several places to search, amazon, goodreads, fan fiction for example, which is still fine.
What actually happens is one or two covers download in a few seconds, and you already know which you want, the other is still downloading.
You select the one you want - and just as you click OK, the other one downloads and you selection Jumps to that one instead. - Is that intended behaviour? Can it be altered to not change your selection?

Edit: Adding more

Column Title - (Allow renaming of set titles or shrink on allingment or remove (MB) from heading)
Reason: The "Size" column, has "Size (MB)" 9 characters wide,
when you adjust it,it shrinks by keeping the colunn heading centered.
So, you end up with an unreadable Title heading or a unneeedfully wide column.

Default Book Cover - Can we have more of these or our own PNG with Transparancy)
Reason: Default cover, the one of a brown book with black spine, 3d look. is great,
it allowe transparancy, shows up in the Book details window on Grey background, and in cover browser on black
It always looks good.
Our Covers are flat and can not have transparancy, Any costom cover we use can never be 3d, or anything but a flat rectangle
We could make one but it would either have to have black or grey background to match either the Coverbowser view or the bookdetails view.
Suggestion is to either allow transparancy for our covers, if thats possible,
or have several user defineable Default covers with transparancy, which we could then use for books with no generic cover.

Plugin window - Make an entry for "User installed Plugins" -
Reason: so you don't have to search through the whole list to try find one you installed and forgot the name of. None of the other many many plugins that are there are of no real intrest to the average user, they just want to find the one they installed and see its settings, and add or remove it.

This is already there, albeit in a different form. Click preferences -> get plugins to enhance calibre. Change the "Filter list" box at the top left to "Installed".

Though thinking about it, adding a checkbox to filter the list of plugins to only installed ones may be worth it, as going the get new plugins route is not very intuitive.

The problem (for me) with a checkbox is that it isn't clear what it would mean. Does it apply only to user-installed plugins? Does it apply to enabled calibre-installed plugins?

I would suggest changing the existing button "Get New Plugins" to say something like "Manage User Plugins". That is what the dialog actually does. I would also consider setting the default to "Installed plugins" instead of "Not installed plugins".

Alternatively, add "Manage User Plugins" to the preferences page, avoiding going to the general plugins page.

The problem (for me) with a checkbox is that it isn't clear what it would mean. Does it apply only to user-installed plugins? Does it apply to enabled calibre-installed plugins?

I would suggest changing the existing button "Get New Plugins" to say something like "Manage User Plugins". That is what the dialog actually does. I would also consider setting the default to "Installed plugins" instead of "Not installed plugins".

Alternatively, add "Manage User Plugins" to the preferences page, avoiding going to the general plugins page.

I like this one. Manage

Might I suggest: Manage Columns (on the column header right-click menu) instead of "Add your own Colums"? Again, this feature is a 'Manage', not just create and Not just limited to Custom User columns.

Series - Have set Series entries for certain book types (or certain entrys have no number prefix)
Reason: When sorting through books you most likely have one of these;
A Novel
A Collection
An Omnibus
A Book in a Series
A Short Story (Novella, Chapterbook, Short Story, etc)

Series Books work fine, but what if you want to label your novels, as "Novels, so as not to get them mixed up with you short stories, and for easy reference?

It would be a real neat solution if the Series column could have some set titles, that have no Number associated. If this is possible in the scope of the program.
Just entering Novel or Collection yourself results in the books being incremented, and selecting a group of them results in them all having a [1]
Other way is to have another custom column. too many of those will melt your brain

Oh While I'm here.

Edit Metadata Picture Adding - Stop Selection Jumping
Reason: When in Edit metadata window, Downloading Covers, you have set a limit on the time you want the search to take, which is fine say 15seconds. You have set several places to search, amazon, goodreads, fan fiction for example, which is still fine.
What actually happens is one or two covers download in a few seconds, and you already know which you want, the other is still downloading.
You select the one you want - and just as you click OK, the other one downloads and you selection Jumps to that one instead. - Is that intended behaviour? Can it be altered to not change your selection?

Edit Metadata Picture Adding - Stop Selection Jumping
Reason: When in Edit metadata window, Downloading Covers, you have set a limit on the time you want the search to take, which is fine say 15seconds. You have set several places to search, amazon, goodreads, fan fiction for example, which is still fine.
What actually happens is one or two covers download in a few seconds, and you already know which you want, the other is still downloading.
You select the one you want - and just as you click OK, the other one downloads and you selection Jumps to that one instead. - Is that intended behaviour? Can it be altered to not change your selection?

Man this has ticked me off at times.
I click my selection and then Ok, only to find that it has changed which was captured and I have to go back and wait out the images again.
I have set a cover priority. please Start With and Leave the covers in that order (I would prefer leaving a 'Blank book cover' for those not found)